Airborne and spaceborne remote sensing of ice freeboard offers a good method of retrieving ice thickness in the polar oceans. However, its accuracy is highly limited by the factors altering the hydrostatic equilibrium of ice floes, such as snow cover and melt ponds which change the surface loading on the ice volume. In contrast to the abundant studies on snow loads, little attention has been paid to the role of melt ponds, partly owing to the difficulties of freeboard measurements during the melt season. To help fill this gap and provide a basis for possible instruments and algorithms being able to access ice freeboard with melting surface in future, a theoretical model was developed to investigate the uncertainty in ice thickness retrieval due to surface melting. First, the ice thickness was related to the freeboard, snow depth, melt pond size and densities of snow, ice and water, and then a sensitivity analysis was carried out to study the influence of melt pond morphology. The results show that melting ice has a much lower mean thickness than ice without a melting surface, although with the same freeboard because of a loss of floe weight due to melting. During pond evolution, a floe gains weight when ponds deepen on the vertical scale, but loses weight when they widen on the horizontal scale, resulting in increasing mean ice thickness with decreasing pond depth and fraction. Freeboard is found to be the major source of uncertainty in the retrieved thickness of first-year ice (FYI), while it is ice density in the case of multi-year ice (MYI). The ratio of ice draft to freeboard ranges from 3.0 to 6.2 for FYI and 2.0 to 4.1 for MYI, agreeing with field observations during melting seasons.